I'm pretty sure the one you are talking about is the one I showed you. I have some old VHS tapes from about 10 years ago with that show and it has been the only Megaman TV series in the past untill Megaman NT Warrior. It does fit your description too, as I remember that Roll called Megaman "Little Bro" and that Protoman was evil (well kind of, in one episode he sided with Megaman but then betrayed him again).